The Latics owner gave his boss Roberto Martinez permission to speak to the Reds and then appeared to be speaking to the media every day to give updates. Swansea's Brendan Rodgers was eventually appointed on Friday, after the manager, Liverpool and the Swans concluded negotiations in less than four days in a much more private affair.
"Our aim from the outset was to conduct a proper, thorough, search and do it in the proper manner," Ayre told the Liverpool Echo. "It is disappointing, then, that Dave Whelan felt the need to run the kind of sideshow he conducted via Sky Sports News and various other media outlets."
He went on: "From our point of view, we did all the right things. We approached the clubs we needed to approach, and conducted ourselves properly at all times... To be honest, I always thought John Bishop was the biggest comedian in the north west but Dave Whelan seems to have taken that mantle over the last couple of weeks."
At one stage last week Whelan claimed Martinez had been made an offer by Liverpool, something Ayre denies.
"That is patently not true," he said. "We make no secret of the fact we spoke with Roberto Martinez, but that is all we did.
"He is a great guy, and I can't speak highly enough of his professionalism and conduct.
"But for his chairman to make suggestions like he has, and suggestions that just aren't true, well it is disappointing to say the least.
"We can say with absolute certainty that the only person who was made any offer by Liverpool Football Club is Brendan Rodgers."
Whelan was unavailable for comment when Press Association Sport attempted to contact him.